Workflow

Parameters used:
gene_ids: ENSG00000TEST
multiple samples: yes
NFLR_mean: 0.3
NFLR_perSample: 0
min_sample_perc: 8

Click the nodes to obtain details about each step.

Post-filtering

Transcript categories

Transcripts ranked

Pre-filtering

Transcript categories

Transcripts detected vs. expression

Statistics

If the workflow has been executed in cluster/cloud, runtimes include the waiting time in the queue.

Configuration

Configuration files
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## General pipeline parameters:

# working directory (required; cannot be an empty string)
workdir: "/tmp_mnt/filer1/bioinformatics/Sid/SCRIPTS_2/Snakemake/PacBio_pipeline/PSQAN/test_output"

# prefix of all output files (required; cannot be an empty string)
sample_name: "testData"

# sqanti "classification.txt" file (required)
sqanti_class: "/tmp_mnt/filer1/bioinformatics/Sid/SCRIPTS_2/Snakemake/PacBio_pipeline/PSQAN/test_data/sqanti_classification.txt"

# sqanti corrected.fasta file (required)
sqanti_fasta: "/tmp_mnt/filer1/bioinformatics/Sid/SCRIPTS_2/Snakemake/PacBio_pipeline/PSQAN/test_data/sqanti_corrected.fasta"

# gene of interest (optional)
# leave as empty string ("") if not using
# multiple genes can be input separated by ";"
gene_ids: "ENSG00000TEST"

######################################################
# transcript thresholds for filtering
# only transcripts with >= thresholds will be retained
######################################################

# does your sqanti file has abundences of more than one sample?
multisample: "yes"

# threshold of NFLR (if one sample) or NFLR_mean across samples (if multisample); default = 0.3
NFLR_mean: 0.3

# threshold of "normalised expression per sample"; default = 0
# Not used if only one sample
NFLR_perSample: 0

# minimum number of samples (%) which should pass NFLR threshold; default = 0
# Not used if only one sample
min_sample_perc: 8

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